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Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis

Figure 4

Subtle conformational changes induced by SAM binding.

(A) Force distribution for backbone hydrogen bonds of helix B indicates helix bending. Hydrogen bonds are plotted as sticks, with red for increasing and blue for decreasing O-H Coulomb interaction. Spheres show the atoms of Ala64, Cys58 and Asn53. The angle between these atoms increases upon SAM binding. (B) Force transmission via a buried salt bridge and quenching of side chain fluctuations for MetJ-dna (left) and MetJ (right). Sticks display average coordinates over 300 ns in the apo (red) and holo (colors by atom type) configuration. Bending of helix B, supported by direct interaction with SAM, puts strain on the salt bridge formed by Glu59 and Arg43, visible as a small conformational rearrangement and high changes in pairwise forces. Fluctuations of Glu39 and Arg42 are quenched due to strong interaction with SAM, see also Fig. 4. (C) Relocation and stiffening of the Arg40 side chain for MetJ-dna (left) and MetJ (right). We measured tighter packing of the Thr37, Arg40 and Asn53 side chains and increased Arg40-DNA salt bridge formation.

doi: https://doi.org/10.1371/journal.pcbi.1000574.g004